Chaparral is the most extensive vegetation type in California. The chaparral vegetation generally experiences larger fluctuations in temperature and slightly greater winter rainfallthan coastal sage scrub. Many chaparral species are slow-growing, dense, woody shrubs with thick leathery leaves and deep root systems. Many have the ability to regenerate after fire.

In San Elijo Lagoon Ecological Reserve, denser and more diverse chaparral is found on the south side above the coastal sage scrub. It extends down to the main trail in only a few places. However, several chaparral shrubs are frequently found in the coastal sage scrub.